Multi-blob coarse graining for ring polymer solutions

We present a multi-scale molecular modeling of concentrated solutions of unknotted and non-concatenated ring polymers under good solvent conditions. The approach is based on a multi-blob representation of each ring polymer, which is capable of overcoming the shortcomings of single-blob approaches that lose their validity at concentrations exceeding the overlap density of the solution [A. Narros, A. J. Moreno, and C. N. Likos, Soft Matter, 2010, 6, 2435]. By means of a first principles coarse-graining strategy based on analytically determined effective pair potentials between the blobs, computed at zero density, we quantitatively reproduce the single molecule and solution properties of a system with well-defined topological constraints. Detailed comparisons with the underlying, monomer-resolved model demonstrate the validity of our approach, which employs fully transferable pair potentials between connected and unconnected blobs. We demonstrate that the pair structure between the centers of mass of the rings is accurately reproduced by the multi-blob approach, thus opening the way for simulation of arbitrarily long polymers. Finally, we show the importance of the topological constraint of non-concatenation on the structure of the concentrated solution and in particular on the size of the correlation hole and the shrinkage of the rings as melt concentrations are approached.This work has been supported by the Austrian Science Fund (FWF), Grant 23400-N16.Peer Reviewe

Atomic motions in the αβ\alpha\beta-region of glass-forming polymers: Molecular versus Mode Coupling Theory approach

We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions (``$\beta$-like'') in addition to the diffusive structural relaxation. A molecular approach provides a direct connection between the local conformational changes reflected in the atomic motions and the secondary relaxations in this polymer. Such local processes occur just in the time window where the $\beta$-process of the Mode Coupling Theory is expected. We show that the application of this theory is still possible, and yields an unusually large value of the exponent parameter. This result might originate from the competition between two mechanisms for dynamic arrest: intermolecular packing and intramolecular barriers for local conformational changes (``$\beta$-like'').Comment: 10 pages, 6 figure

Winding angle distributions for two-dimensional collapsing polymers

9 pages, 5 figures, (this version: email address corrected

Presentaciones de los investigadores del CSIC en la jornada.

Jornada de DARIAH en la Biblioteca Nacional de España desarrollada el martes, 7 de noviembre de 2023 de 16:00h -19:30h. De los pósters presentados, los siguientes 14 pertenecen a de proyectos del CSIC: 1) Veinte años de Humanidades Digitales; 2) Proyecto Alisos. Las redes alimentarias sostenibles como cadenas de valores para la transición agroecológica y alimentaria: implicaciones para las políticas públicas territoriales; 3) Argos. Un buscador sintáctico en treebanks grecolatinos; 4) CORHIJE- DHJE APP. Herramienta digital para la creación del Corpus y Diccionario Histórico del Judeoespañol; 5) Diccionario Digital del Griego Antiguo; 6) DIGITESC. Digitalización, descripción y puesta en línea de la colección de manuscritos griegos de El Escorial; 7) IAT/ML y LogosLink. Discursos polarizados; 8) EuQu - The European Qur'an. Islamic Scripture in European culture and religion 1150-1850; 9) Guinzé Sefarad: Archivo documental de la Sefarad medieval; 10) Marcadores afectivos en las cartas transatlánticas de mujeres en la época moderna; 11) Maritime History Map: Proyecto SIC sobre Patrimonio sumergido; 12) La movilidad geográfica y profesional de los sabios musulmanes en la Edad Media: un análisis desde las Humanidades Digitales; 13) PARAHeB - Paratexts Hebrew Bible: understanding the paratexts of the Hebrew Bible; 14) Fuentes gráficas para la reconstrucción virtual en arquitectura: el Gran Palacio de Constantinopla y las miniaturas del Skylitzes Matritensis VITR / 26 / 2.N

Estudio de los movimientos moleculares en polibutadienos con distinta microestructura mediante simulaciones de dinámica molecular y técnicas de neutrones

El marco general de este trabajo es la caracterización a nivel microscópico de la estructura y la dinámica de los Polibutadienos mediante el uso combinado de técnicas neutrónicas y simulaciones atomísticas de dinámica molecular. Los Polibutadienos presentan varias microestructuras monoméricas relativamente sencillas que los hacen candidatos ideales para el estudio de la influencia de la microestructura en el fenómeno de la transición vítrea. Las contribuciones de las distintas unidades conformacionales presentes en esta familia de polímeros a la estructura medida por dispersión de neutrones son exhaustivamente diferenciadas en esta memoria. Asimismo, temas de reciente actualidad como el "crossover" Gaussiano, la heterogeneidad dinámica y el Alpha-Beta merging se discuten en el marco de varios modelos fenomenológicos. En concreto, se propone un modelo que incluye movimientos localizados que se han podido explorar por primera vez con gran detalle a nivel atomístico gracias a la poderosa combinación de las simulaciones con la espectroscopía de neutrones. Por otro lado, se comprueba la validez de una teoría ampliamente discutida en esta área de conocimiento, conocida como "Mode Coupling Theory (MCT)", para incorporar dichos movimientos localizados en la descripción general de la dinámica de este tipo de sistemas. En esta memoria se apunta a la posibilidad de que el origen de los movimientos localizados aquí descritos pueda ser más complejo que el simple "efecto caja" que postula la MCT e incluya cambios conformacionales diferenciados, característicos de los diferentes entornos microestructurales.Peer reviewe

Architecture-induced size asymmetry and effective interactions of ring polymers: Simulation and theory

We investigate, by means of Monte Carlo simulations, the role of ring architecture and topology on the relative sizes of two interacting polymers as a function of the distance between their centers-of-mass. As a general rule, polymers swell as they approach each other, irrespectively of their topologies. For each mutual separation, two identical linear polymers adopt the same average size. However, unknotted rings at close separations adopt different sizes, with the small one being >nested> within the large one over long time intervals, exchanging their roles in the course of the simulation. For two rings of different architectures and identical polymerization degree, the knotted one is always smaller, penetrating the unknotted one. On the basis of these observations, we propose a phenomenological theory for the effective interactions between rings, modeling them as unequal-sized penetrable spheres. This simple approximation provides a good description of the simulation results. In particular, it rationalizes the non-Gaussian shape and the short-distance plateau observed in the effective potential between unknotted ring polymers and pairs of unequal-sized unknotted/knotted ones. Our results demonstrate the crucial role of the architecture on both the effective interactions and the molecular size for strongly interpenetrating polymers. © 2013 American Chemical Society.This work has been supported by the European Community’s Seventh Framework Programme (FP7/2007-2013) under the IEF-RINGEFF, Grant Agreement 236664, and by the Austrian Science Fund (FWF), Grant 23400-N16.Peer Reviewe

Effective interactions of knotted ring polymers

In the present article, we review recent computational investigations on the properties of ring polymers in solution. In particular, we focus on effective interactions obtained by means of coarse-graining techniques. We discuss the relative importance of the self-Avoidance and the topological contributions in the qualitative features of the effective potential. We extend our previous results on identical rings and determine the effective potential between dissimilar ring polymers of distinct topology and size. The results obtained reveal the dramatic effects of the specific topology on the effective interactions, and hence in the structural correlations, of polymeric systems. © 2013 Biochemical Society.This work has been supported by the European Community's Seventh Framework Programme (FP7/2007–2013) under the IEF-RINGEFF [grant number 236664] and by the Austrian Science Fund (FWF) [grant number 23400-N16].Peer Reviewe

Effects of knots on ring polymers in solvents of varying quality

We employ extensive computer simulations to investigate the conformations and the interactions of ring polymers under conditions of worsening solvent quality, in comparison with those for linear polymers. We determine the dependence of the Θ-temperature on knotedness by considering ring polymers of different topologies. We establish a clear decrease of the former upon changing the topology of the polymer from linear to an unknotted ring and a further decrease of the same upon introducing trefoil- or 5-fold knots but we find no difference in the Θ-point between the two knotted molecules. Our results are based on two independent methods: one considering the scaling of the gyration radius with molecular weight and one based on the dependence of the effective interaction on solvent quality. In addition, we calculate several shape-parameters of the polymers to characterize linear, unknotted, and knotted topologies in good solvents and in the proximity of the Θ-point. The shape parameters of the knotted molecules show an interesting crossover at a degree of polymerization that depends on the degree of knottedness of the molecule. © 2013 American Chemical Society.The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under the IEF-RINGEFF, Grant Agreement 236664, and by the Austrian Science Fund (FWF), Grant 23400-N16.Peer Reviewe

Fluids of semiflexible ring polymers: effective potentials and clustering

We present a computational investigation of the structural properties of a fluid of semiflexible ring polymers. Stiffness is introduced by implementing intramolecular barriers. Because of these barriers, shrinkage of the rings is energetically unfavourable, and the ring size can exhibit a non-monotonic density dependence. At high concentrations the rings can swell and adopt open configurations that facilitate interpenetration and clustering. We obtain effective potentials between the centers-of-mass of the rings at infinite dilution, and explore their validity over the whole range of concentrations. Except for the limit of small rings, the effective fluid of ultrasoft particles provides a good description of the real system over a considerable range of densities, even above the overlap concentration. In particular the clustering behaviour predicted by the effective description is observed in the real system for a certain range of molecular masses. However, the effective description is incomplete. Inspection of the clusters of real rings reveals that these can arrange in a complex disordered phase formed by long columns of oblate rings, which are penetrated by bundles of elongated prolate rings. These anisotropic features of the real system are not captured by the standard effective approach, which only considers macromolecular centers-of-mass. This suggests the need to include the relative orientation between rings in the effective potentials. This journal is © 2013 The Royal Society of Chemistry.We acknowledge financial support for the projects MAT2007-63681 (Spain) and IT-436-07 (GV, Spain), and by the Austrian Science Fund (FWF) under Project No. P 23400-N16.Peer Reviewe